Whispers in the Dark
by ErisRocks
Summary: This takes place at the end of season 3 but before 'Sunday' and will be an AU season 4. The Replicators are openly attacking human worlds and Sheppard is captured by the Wraith. Please RnR I need to know what you guys want :D
1. A Bright and Sunny Day

Hello Everyone, I'm back with a brand new fic…Well, not new really, I've been toying with this idea ever since "The Hive" aired. So anyway I'm hoping that it'll be a long one, and I would love to hear feedback from you guys. :D

Chapter 1: A Bright and Sunny Day

_Another day, another briefing. _Lieutenant Colonel John Sheppard thinks as he makes his way towards the briefing room. He quickly jogs up the stairs leading towards the control room and veers left into the briefing room. The ancient doors automatically swing open when they sense his approach. Already inside are his teammates Specialist Ronon Dex and the leader of the Athosians Teyla Emmagan. John quickly sits down as Doctor Elizabeth Weir, leader of the Atlantis Expedition, enters the room. She quickly nods to John, Teyla and Ronon and takes her seat. The team shuffles around a bit as they wait for the self-proclaimed genius Doctor Meredith Rodney McKay to join the briefing.

"So…did anyone catch movie night last week?" John questions to break the silence.

Teyla is the first to respond.

"Yes, I believed Major Lorne called it 'Anaconda,' although I must confess I was confused as to why your people enjoy watching others being devoured by snakes."

"The people on your planet have a weird sense of entertainment Sheppard." Ronon supplies helpfully.

His friends momentarily boggle John, and he casts a nervous glance at Elizabeth only to find her leaning forward in her seat, her arms folded on the table and her eyebrow cocked in amusement. As if to say _You're on your own Sheppard._ Once again his team is ganging up on him. John is only glad to have some sort of relief, as Rodney has still not arrived in order to make his own contribution towards the discussion. John took a deep breath and was about to respond when Rodney McKay came barreling in through the doors talking at a mile per minute. From what John was able to gather it had something to do with the conduits lining the Southern Pier that were damaged by the storm two years ago. They only just got to start repairs due to more pressing matters involving the Replicators.

"Rodney." John sighs as the scientist continues to speak at a phenomenal rate.

"Talking to her," Rodney snaps back, as he points with a frown towards his headset. After one more belittling comment at the poor scientist on the other end Rodney clicks off his headset and sits at the table. "So what were we talking about?"

John is quick to open his mouth to answer back with a witty remark, when Elizabeth beats him to the punch stating. "We were just about to start the briefing on today's mission, to MRX-P37." She quickly darts her eyes to lock onto John's daring him to add anything. Knowing when to stop John leans back in his chair and crosses his arms, smirking at Elizabeth who shakes her head and begins the briefing.

**2 hours later**

John and his team step through the Stargate to the world known as MRX-P37 or Kolona as the natives called it. The area surrounding the gate was lush with fertile fields of green grass surrounding it and the native flora, which resembled fir trees, creating a sort of pathway towards the village that could just be seen in the distance. According to their previous recon missions the people who resided here were friendly and open to trade negotiations. As the flag team of the off world travelers it was their job to make first contact and express an interest in trade. Elizabeth had instructed them to offer medical supplies and manpower, kindly offered by the Athosians, to aid the Kolonians in their struggles to rebuild their settlement after their latest culling. That was proven to be much more ferocious then the previous ones.

John instructs his team to move out towards the village. Unfortunately, the various pollens in the air soon begin to trigger an allergic response in Rodney as they walk towards the village.

"Argh, flowers why are there always flowers?" Rodney bitterly complains as he sneezes into his handkerchief.

Teyla sympathetically pats Rodney on the back as they continue walking, while Ronon and John share an exasperated look as Rodney continues to gripe and moan about his allergies and other problems. John soon tunes out his friend as he concentrates on getting to the village as quickly as possible.

John removes his sunglasses as they arrive in the broken remains of a once bright and cheerful village. The villagers are hard at work repairing their houses and other buildings. Although they are but a small farming community the village is beginning to look more like its former self. They are not waiting for long as a small, wizened man emerges from one of the completed huts. He hobbles towards them, a walking stick in one hand, and the other clutching the arm of a younger man, leading him towards the Atlantians. Both are tanned, the younger with short, dark and curly hair, and the elder with shoulder length, wavy, salt and pepper coloured grey hair.

John is the first to speak to the man, whom he believes to be the leader of the village. "Hi, my name is Lieutenant Colonel John Sheppard and this is Teyla Emmagan, Ronon Dex and Doctor Rodney McKay."

The small man stumbles forward a few more paces before addressing John.

"Greetings, I am Tolan leader of this village and this is my son Roland," His wrinkled features twist into a smile and his watery eyes fix themselves onto the team's clothing. "You must have traveled far, I have not seen such clothes among the traders of this world, come join me for some tea and we shall speak of trade."

John and his team exchange confused glances at the old man's statement, but never the less follow him into the nearest house. Once inside the poorly lit building Tolan gestures them forward to sit at the table, as Roland disappears through another door, returning only a minute later with the tea.

"Thank-you my boy, some of you best yet." Tolan praises his son as he takes a sip of the tea.

John swirls the tea around in its small cup, the leaves sticking to the sides and giving off a strong smell. John grimaces remembering drinking the tea the Athosians made with some type of grass, native to Athos, he couldn't keep anything down for two days. Slowly John lowers the cup back to the table and addresses Tolan.

"If you don't mind me asking, how long ago was it when the Wraith attacked your village?" John questions carefully, Elizabeth would have his head if he were to offend potential allies.

"One lunar cycle, my people have been working quite industriously in order to rebuild what we once had, but I'm afraid you are mistaken Colonel about who is responsible for this atrocity." Tolan replies, sipping his tea.

The team simultaneously look up at Tolan, surprise etched onto their features. Recovering his voice Rodney speaks first "If it wasn't the Wraith then who could've possibly…"

"They were men," Tolan interjects "At least that's what we first thought, they approached us not from the Ring but the sky…at least that's what we assumed."

John and his team listen closely as Tolan gives what could potentially be intel on a whole new threat _As if the Wraith and the Replicators weren't enough of a threat_ John thinks.

"They appeared out of nowhere in the village one day, the three of them dressed in white garments, two men a tall one with yellow hair, a shorter fiercer one and a woman with sandy brown hair and cold, calculating eyes. We were ignorant of their intentions; curiosity got the better of us. When we attempted to approach them the woman spoke in a foreign tongue into a band on her wrist. That's when the ships came," Tolan pauses in his speech to cough loudly, startling them.

"Please, tell us more of these strangers." Teyla speaks quickly and quietly to Tolan.

"And those ships." Adds Rodney.

"The ships descended from the sky, then they opened fire onto the larger areas of the village, the blasts hit all around us, destroying homes and killing many. The men disappeared, and only the woman remained calmly watching the destruction. Once it was over she walked up to one of the other men in the village and placed her hand in his head. It was obvious to us all that she was not human. Once she was done with him she removed her hand and turned to me she told me to tell others of what I had witnessed today, she said it was the beginning of the end, that the reign of the Wraith would end and the Replicators would take what was rightfully theirs." Tolan finishes gravely.

Everyone in the room is stunned; suddenly John leaps to his feet.

"I'm sorry Tolan, but we will need to communicate this with our leader. Lets go guys." John hurriedly speaks in one breath.

"Of course," Tolan replies "We will see you later for trade negotiations then?"

"Trade? Yes of course we will be back within the hour."

Tolan bids them farewell as the team make their way back to the Stargate.

"Can you believe that?" Rodney babbles, "The Replicators spared them to tell other worlds of their plan, it's so surreal. I mean what are they playing at?"

John looks confused, as do Ronon and Teyla and the rest of the journey back to the Stargate is made in silence. Once the Stargate is in sight Rodney rushes up to it to begin the dialing sequence. But before he can do so symbols on the DHD light up.

"Incoming wormhole!" Rodney shouts as he races back towards them and the wormhole is locked. With a terrible scream a dart comes racing through the event horizon, towards the village. The team raises their guns in order to fire upon the vessel. However, the dart is too quick and races towards the village, then unexpectedly it doubles back and releases a culling beam as it swoops towards them.

"Scatter!" John yells, pushing Rodney towards the tree line as the dart closes in.

Ronon and Teyla race towards the trees firing their weapons as they went. Terrifies for their teammates, as the dart gets closer. Rodney barely manages to escape the beam, as he dives out of the way. John was not as fortunate. Once getting what it apparently came for the dart then races through the still active Stargate. Fear and horror etched into his features Rodney scrambles towards the DHD before the Stargate disengages. Just as he arrives the wormhole disengages and the symbols disappear before Rodney could see.

Panting Ronon and Teyla rush up to Rodney, now looking thoroughly lost.

"Did you get it?" Ronon pants as his reaches Rodney.

When he doesn't respond Teyla asks him "Rodney did you see the symbols?" The Athosian looks concerned for her friend as he fails to speak.

"I-I…No. Look we need to get Zelenka out here, with a jumper. We need to hurry there's no telling where that dart went or where it's taking Colonel Sheppard!"

Nodding in agreement Ronon walks up to the DHD and dials Atlantis.

So what do you think? :D Nothing but good things I hope. I really need feedback on this guys, I'm not really sure where this is going or what you guys want so pleassseee R n R. :D please.


	2. Not Again

I'm so very sorry for the long wait with this chapter guys, but the magic fairy of inspiration has clobbered me over the head and I shall now be updating much more frequently. Thank you to everyone who has stayed with this fic and I hope you all enjoy it. All right and here is the second chapter and big amazing thank you to all my reviewers, I hope you like it.

As for everyone else I just hope that you enjoy it too, feel free to ask questions and tell me what you think. Reminder to everyone this is a romance so please don't kill me when the leading lady isn't who you may have wanted or pictured.

**Chapter 2: Not Again**

In Atlantis the Stargate activates with a great roar. Chuck, the Gate Technician, checks the computer screen next to his workstation for the IDC.

Surprised he looks up at Elizabeth as she walks up to him from her office. "It's Ronon's IDC, ma'am."

"They're not due to return for three hours…well, then I guess there is a first time for everything. Let 'em in." Elizabeth smiles at Chuck, before walking down the Lantian stairs to greet the team.

Before she can get a word in Rodney, followed by Teyla and Ronon, comes out of the event horizon, agitated and already briefing Elizabeth.

"Rodney, slow down, where's Colonel Sheppard." Elizabeth exclaims in confusion gesturing towards the team.

Not one to be deterred Rodney continues speaking "That's what I've been trying to tell you. He's gone."

Even more confused Elizabeth replies, "Gone, what do you mean he's gone!"

"The Wraith," he elaborates "we were coming back to tell you about some key intel we got from the planet, when the gate activated and a dart appeared. It swooped us, turned back and took Sheppard!"

Elizabeth opened her mouth to respond when Teyla gently interjected. "Elizabeth, perhaps it would be best if we continued this discussion another time," she then turns to Rodney "Rodney did you not say that it was a matter of great importance that we procure the last address dialed from the planet."

Snapping his fingers Rodney speaks "Yes, yes, yes. We need Radek and a team of scientists out there as soon as possible, I could do it myself but we may not have the time."

Elizabeth frowns slightly, confused as to why Rodney would want anyone but himself retrieving the address. "Not enough time? Rodney what are you talking about?"

Completely devoid of any emotion, Rodney deadpans "Elizabeth, it's the Replicators."

In that moment Elizabeth was sure she could feel all the oxygen leaving the room as she stared back at Rodney in stunned silence. After a few seconds, after what seemed like an eternity, Elizabeth addresses Rodney once again.

"The Replicators? What do they have to do with Colonel Sheppard or the planet?" she questions, becoming even more anxious by the minute.

Being all too aware of the time constraints they are under Rodney shakes his head and replies "We don't have time for this right now! We need to get back to that planet and get the address, look in the time it'll take to get the potential addresses and assemble the search teams the Wraith could have taken Sheppard anywhere. Oh, and that's the least of our problems 'cause the Replicators are out there right now decimating the human populations of the entire galaxy!"

Leaving no time for a response Rodney quickly exits the gate room and heads off towards his lab, already briefing Radek on the current situation. Quickly recovering from Rodney's tirade Elizabeth turns to Teyla and Ronon, who for the most part had been silent throughout the recent turn of events.

"I want both of you to report to the infirmary for your post mission check ups." Elizabeth orders the remaining two members of the flagship team of the Atlantis expedition. As Ronon opens his mouth to issue some form of protest, Teyla gently places her hand on his tense arm, as Ronon looks at the petite Athosian they lock gazes and with a slight nod of her head Teyla then leads the non-protesting ex-Runner from the Gate Room towards the infirmary.

Meanwhile on board the Hive ship

John awoke to discover that he was once again taken captive by the Wraith. With a soft sigh he struggles to sit up as he notices the fatigue still gripping his body, as the Wraith beam gave out a stunning effect and thus caused the victims of a culling to wake up dead, or cocooned in the Hive ship.

As John sat up his military training began to kick in and he noticed his surroundings in the cell...Nothing, great. It would appear that the Wraith had especially prepared this cell for Sheppard's arrival, knowing of his reputation as a murderer, rather than the hero most of the galaxy saw him as.

"Well," he drawled "this is new."

John paused and looked around the cell before realising, with a shake of his head, that the walls weren't likely to talk back. Sighing John stood upon shaky feet and slouched against the wall waiting for something anything to happen.

Cut to Atlantis

Rodney was busy in his lab, usually this was no surprise but today however the stakes were higher than a simple 'Elizabeth, I've turned Sheppard invisible.' How Rodney longed for one of those days. He was busy at his work station attempting to recalibrate the city's sensors to pick up nanites and Colonel Sheppard's transmitter. Rodney was hoping that his theory was wrong and there was infact a rogue Replicator faction out causing trouble and not the entire planet. Furthermore he also hoped that John's tracker was still funtional and the Wraith had no way to remove it but as it so happened fate was not on Rodney's side today.

Hive Ship

John was just settling down for a quick nap when he was jerked from his slumber by the sound of the cell doors opening. Sheppard's eyes snapped open and he came face to face with a shocking sight the commander of the Hive. He had, as was typical for a wraith, long white hair that was left loose and spilled over his shoulders to his pecs. His face bore no markings but there was a tattoo on his right hand of a wraith letter or number, Sheppard couldn't read wraith and was obviously at a disadvantage to know what it meant. The commander's body was encased in the traditional black leathers that befitted his station. With a rumbling hiss the commander gestured at John to follow him, the two drones that he had with him waiting for John to follow the commander before following him in turn. John slowly rose and began analysising his chances of overpowering the two guards and successfully making it to the dart bay before the alarm was raised and the other drones were sent to recapture him. John concluded that his chances were less than slim if he somehow managed to overpower the burly guards and escape. Therefore, John decided that it was best for the meantime to sit tight and wait until a better opportunity presented itself to escape. If there was one thing that John knew about the wraith it was that they were arrogant believeing themselves to be superior to humans in every way and therefore would eventually let their guard down around him and that would be when John would strike. It wasn't a brilliant plan but it was a plan none the less.

Seeing no other alternative John walked out the door and followed the commander through many different corridors, passing many smirking wraith as they did so until they came to a webbed doorway that opened at the commander's approach. The commander stopped just inside the door and the two drones grabbed John roughly by the shoulders and forced him into a contraption that looked more than passingly like an electric chair. John was strapped in and the commander walked over to a console by the wall next to the chair and poked at a few buttons before sticking his hands into some weird knobby things that looked like joysticks and proceeded to make the machine wirr and bing. Then John felt a searing pain in the back of his neck at bit his lip to keep from screaming as a sharp device peeled back the skin and pulled out his tracker. John then realised in horror that his friends would no longer be able to find him if the tracker was disabled. The commander smiled as though having read John's mind and then returned his attention to the console before entering a series of button pushes and tugs on the joystick and John felt his skin being sewn back together and a gelatinous goo being slathered on the wound before the chair released him and the two drones caught him in their vice like grip, before dragging him out the door and back through the twisting corridors before taking him back to his cell. Upon arrival John noticed that the room now contained two blankets and a bowl with a grey paste inside it. The blankets John noticed as he picked them up in his hands, were rough and course, as he laid them out in the corner of the cell so John could watch the door, but still hide in the shadows of the cell, if necessary. Once set up John then walked over to the bowl and hefting it up into his hands he gingerly poked a finger into the paste and tasted it. It wasn't so bad bland but he was certain full of whatever nutrients he needed to stay alive. The only thing that John knew that he would not be receiving would be vitamin D as John was sure that the ship wouldn't land and he wouldn't be allowed to leave it. John sighed to himself and finished off the rest of the bland paste before curling up on the blankets and falling asleep.

Meanwhile in Atlantis Rodney was just finishing up on the final bit of calibrating that would allow him to track John, unfortunately for Rodney the Colonel had already had his transmitter removed and was now likely to never be found by his friends. With a few stokes on his keyboard Rodney finished the calibrations and discovered the fate of his friend was completely unknown and was likely to never be found.

"Oh no," Rodney muttered as he gazed in horror at the screen, realising that he could do nothing to help his friend. Tapping his ear piece Rodney spoke to Elizabeth in the control room "Elizabeth, I'm gonna need to see you right away. It's about John." With that Rodney turned and walked from the room leaving the blank screen inactive behind him.

As Rodney walked the distance to the control room he was tortured by images of what vile and horrid things the wraith were doing to John. Worried out of his mind Rodney finally arrived in the control room and felt the eyes of everyone in the control room on him, it was very uncomfortable. Rodney jogged up the stairs of the control room to meet Elizabeth halfway as she came down towards him, hope written all across her lovely features and Rodney felt guilt welling up within him that he could do nothing to help John.

"Elizabeth," Rodney began as he looked around the assembled in the control room who were all holding their breath collectively as they waited to hear what Rodney had to say. "he's gone. I recalibrated the city's censors to pick up his tracker but..." Rodney took a deep breath to steel himself as he delivered the final blow. "there's nothing, the wraith must've found a way to deactivate it because I can't find him. It's as if he never even existed."

Elizabeth took the news with stride her face betrayed no emotion but if one was to look closely into her eyes the split second in which Rodney told her that John was lost forever they would see heartbreak and gut wrenching sadness. Elizabeth nodded her head and turned to walk into her office Ronon and Teyla watching her go. Rodney, however turned his gaze to the floor and at this Teyla was spurred into action. She walked up to Rodney and wrapped her arms around his slightly shaking form Ronon sending glares around the control room ensuring that no one would destroy this tender moment. Taking the hint the various technicians all returned to their various tasks and left the team and the city's leader to their grief.

After a few minutes Rodney broke away from the comforting embrace of the Athosian woman and smiled slightly at her before his eyes lit up with a brilliant idea.

"The sensors! Oh, why didn't I think of it before, we that is I can recalibrate the city's sensors to pick up on the residual radiation left from replicator weapons fire, don't you guys see what this means!" Rodney asked a broad smile on his face.

"What is it Rodney? I do not understand." Teyla spoke for both herself and Ronon who were giving the scientist confused looks.

"We might be able to track the replicator ships and find out their next target. It's a long shot at best but I believe that we can do it!"

"This is great news then Rodney." Teyla said as she smiled at the physicist. "With this information we may be able to save countless lives."

"Yeah, yeah!" Rodney said optimistically happy that they will be able to forge on ahead and do good in the galaxy with or without their beloved team leader.

A/N: and so that concludes that chapter I know that it has been hugely overdue but I didn't want to publish a half hearted fic and this way everybody wins and fear not I shall continue it please read and review. :D


End file.
